| Previous changeset 0:902ab790fb7b (2017-02-23) |
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Commit message:
Uploaded |
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modified:
TableMerge/tablemerge.xml TableMerge/tablemerge_wrap.R |
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added:
TableMerge/README.md |
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removed:
TableMerge/README.txt |
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| diff -r 902ab790fb7b -r e44c5246247a TableMerge/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TableMerge/README.md Thu Nov 14 12:33:41 2019 -0500 |
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| @@ -0,0 +1,52 @@ +Table Merge +======= + +Metadata +----------- + + * **@name**: Table Merge + * **@version**: 1.0.1 + * **@authors**: Melanie Petera (PFEM - INRA - MetaboHUB) + * **@init date**: 2015, June + * **@main usage**: This tool merges a data matrix file with a selected metadata file to obtain a single file. + + +Context +----------- + +This tool is provided as one of the [Workflow4Metabolomics](http://workflow4metabolomics.org) Galaxy instance statistical tools. +W4M is a French infrastructure providing software tools to process, analyse and annotate metabolomics data. + +User interface is based on the Galaxy platform (homepage: https://galaxyproject.org/). It is an open, web-based platform for data intensive biomedical research. +Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. + + +Configuration +----------- + +### Requirement: + * R software: version > 3.0.0 recommended + * Specific R libraries: 'batch' + + +Technical description +----------- + +Main files: + +- tablemerge_script.R: R function (core script) +- tablemerge_wrap.R: R script to link the main R function to inputs +- tablemerge.xml: XML wrapper (interface for Galaxy) +- RcheckLibrary.R and miniTools.R: additional R functions used by the core script (input checks and data handling) + + +Services provided +----------- + + * Help and support: support@workflow4metabolomics.org + + +License +----------- + + * Cea Cnrs Inria Logiciel Libre License, version 2.1 (CECILL-2.1) |
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| diff -r 902ab790fb7b -r e44c5246247a TableMerge/README.txt --- a/TableMerge/README.txt Thu Feb 23 04:37:49 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,39 +0,0 @@ -## ****** Table Merge environment: ****** ## -# version 2016-07-20 M Petera - -## --- PERL compilator / libraries: --- ## -NA --- - -## --- R bin and Packages: --- ## -$ R --version -R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" -Platform: x86_64-redhat-linux-gnu (64-bit) - -The dependent libs are : -library(batch) --- - -## --- Binary dependencies --- ## -NA --- - -## --- Config: --- ## -NA --- - -## --- XML HELP PART --- ## -NA --- - -## --- DATASETS --- ## -No data set ! waiting for galaxy pages --- - -## --- ??? COMMENTS ??? --- ## -!WARNING! : Its existence made obsolete the old "Filters" tool --- - -## --- Changelog/News --- ## -NA --- \ No newline at end of file |
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| diff -r 902ab790fb7b -r e44c5246247a TableMerge/tablemerge.xml --- a/TableMerge/tablemerge.xml Thu Feb 23 04:37:49 2017 -0500 +++ b/TableMerge/tablemerge.xml Thu Nov 14 12:33:41 2019 -0500 |
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| @@ -108,10 +108,6 @@ --------------------------------------------------- ---------------- -Working example ---------------- - .. class:: warningmark |
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| diff -r 902ab790fb7b -r e44c5246247a TableMerge/tablemerge_wrap.R --- a/TableMerge/tablemerge_wrap.R Thu Feb 23 04:37:49 2017 -0500 +++ b/TableMerge/tablemerge_wrap.R Thu Nov 14 12:33:41 2019 -0500 |
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| @@ -7,7 +7,8 @@ # User: Galaxy # # Original data: used with tablemerge_script.R # # Starting date: 11-05-2015 # -# V-1: Firt version of wrapper # +# V-1: First version of wrapper # +# V-2: Addition of prints about input parameters and job info # # # # # # Input files: dataMatrix ; Metadata file # @@ -31,8 +32,22 @@ if(length(args) < 4){ stop("NOT enough argument !!!") } +cat('\nJob starting time:\n',format(Sys.time(), "%a %d %b %Y %X"), +'\n\n--------------------------------------------------------------------', +'\nParameters used in "Table Merge":\n\n') +print(args) +cat('--------------------------------------------------------------------\n\n') + + tab.merge(args$dataMatrix_in, args$Metadata_in, args$metatype, args$combined_out) +cat('\n--------------------------------------------------------------------', +'\nInformation about R (version, Operating System, attached or loaded packages):\n\n') +sessionInfo() +cat('--------------------------------------------------------------------\n', +'\nJob ending time:\n',format(Sys.time(), "%a %d %b %Y %X")) + + #delete the parameters to avoid the passage to the next tool in .RData image rm(args) |